How can I automate this kind of Blender 2D animations?
Blender can do many of the effects seen in this video, but the drawing and colouring in effect is  screen capture.
Having said that you can sort of fake it by capturing a drawn frame, using Grease Pencil in the VSE preview window. Grab it by rendering with the OpenGL render button. Thats the little camera button highlighted in yellow.



You can re-import this frame and wipe it on over the clean frame. Remember to turn off the Grease Pencil layer.